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PssmInput Class Reference

Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix). More...

Public Member Functions

 PssmInput ()
 Default constructor.
 
 PssmInput (istream &is)
 istream constructor.
 
 PssmInput (const PssmInput &orig)
 Copy constructor.
 
virtual ~PssmInput ()
 Destructor.
 
virtual void copy (const PssmInput &orig)
 Copy orig object to this object ("deep copy"). More...
 
virtual PssmInputnewCopy ()
 Construct a new "deep copy" of this object. More...
 
PssmInputoperator= (const PssmInput &orig)
 Assignment operator. More...
 
double score (int i, int j)
 Return the score of the aminoacid j in position i.
 
virtual unsigned int size () const
 Return the size of the object referred as the dimension of the PSSM.
 

Static Public Member Functions

template<class T >
static void pReadDoubleVector (istream &is, vector< vector< T > > &data, vector< string > &data1, vector< string > &data2)
 Helper function used to read a vector<vector> construct. More...
 
template<class T >
static void pWriteDoubleVector (ostream &os, vector< vector< T > > data, vector< string > data1, vector< string > data2)
 Helper function used to write a vector<vector> construct. More...
 

Friends

ostream & operator<< (ostream &os, const PssmInput &object)
 Output operator. More...
 
istream & operator>> (istream &is, PssmInput &object)
 Input operator. More...
 

Detailed Description

Implement I/O objects for handling BLAST PSSM (Position Specific Score Matrix).

Member Function Documentation

void copy ( const PssmInput orig)
virtual

Copy orig object to this object ("deep copy").

Parameters
orig
PssmInput * newCopy ( )
virtual

Construct a new "deep copy" of this object.

Returns
PssmInput & operator= ( const PssmInput orig)

Assignment operator.

Parameters
orig
Returns
template void pReadDoubleVector ( istream &  is,
vector< vector< T > > &  data,
vector< string > &  data1,
vector< string > &  data2 
)
static

Helper function used to read a vector<vector> construct.

Parameters
is
data
data1
data2
void pWriteDoubleVector ( ostream &  os,
vector< vector< T > >  data,
vector< string >  data1,
vector< string >  data2 
)
static

Helper function used to write a vector<vector> construct.

Parameters
os
data
data1
data2

Friends And Related Function Documentation

ostream& operator<< ( ostream &  os,
const PssmInput object 
)
friend

Output operator.

Parameters
os
object
Returns
istream& operator>> ( istream &  is,
PssmInput object 
)
friend

Input operator.

Parameters
is
object
Returns

The documentation for this class was generated from the following files: